Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012317.1 Kokia drynarioides strain JFW-HI SEQ_127319, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 203848
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:9911 original size:15 final size:16
Alignment explanation
Indices: 9886--9939 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
9876 TGGAGTGGAA
*
9886 AGAAAATTAGAAGGAT
1 AGAAAAATAGAAGGAT
*
9902 -GAAAAATAGAAGGGGT
1 AGAAAAATAGAA-GGAT
*
9918 AGAAAACTAGAAGGAT
1 AGAAAAATAGAAGGAT
*
9934 GGAAAA
1 AGAAAA
9940 CATAAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 10 0.32
16 11 0.35
17 10 0.32
ACGTcount: A:0.56, C:0.02, G:0.30, T:0.13
Consensus pattern (16 bp):
AGAAAAATAGAAGGAT
Found at i:15163 original size:22 final size:24
Alignment explanation
Indices: 15138--15183 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
15128 TTTTTCAAAA
*
15138 AAATC-GAAATGTATT-TTTTTAT
1 AAATCAGAAATGAATTGTTTTTAT
*
15160 AAATCATAAATGAATTGTTTTTAT
1 AAATCAGAAATGAATTGTTTTTAT
15184 TTATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 8 0.40
24 7 0.35
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (24 bp):
AAATCAGAAATGAATTGTTTTTAT
Found at i:18872 original size:97 final size:97
Alignment explanation
Indices: 18706--18896 Score: 337
Period size: 97 Copynumber: 2.0 Consensus size: 97
18696 TGAAAAAAAA
18706 GGTATTCGATTATCCCGGTTTGAAGAAAAATAGCGCCTAGTAAGTTAAGGCACAAATTTCCAAAA
1 GGTATTCGATTATCCCGGTTTGAAGAAAAATAGCGCCTAGTAAGTTAAGGCACAAATTTCCAAAA
*
18771 CCCGATATAAAGGAATATTGCCTCGATTTAAG
66 CCCGAGATAAAGGAATATTGCCTCGATTTAAG
* * * *
18803 GGTATTCGATTATCCCGGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGTACAAATTTTCAAAA
1 GGTATTCGATTATCCCGGTTTGAAGAAAAATAGCGCCTAGTAAGTTAAGGCACAAATTTCCAAAA
18868 CCCGAGATAAAGGAATATTGCCTCGATTT
66 CCCGAGATAAAGGAATATTGCCTCGATTT
18897 TAAATATTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (97 bp):
GGTATTCGATTATCCCGGTTTGAAGAAAAATAGCGCCTAGTAAGTTAAGGCACAAATTTCCAAAA
CCCGAGATAAAGGAATATTGCCTCGATTTAAG
Found at i:19045 original size:14 final size:15
Alignment explanation
Indices: 19026--19060 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
19016 AGCACGAATG
*
19026 AATAAATATACG-AA
1 AATAAATATAAGAAA
19040 AATAAATATAAGAAA
1 AATAAATATAAGAAA
19055 AATAAA
1 AATAAA
19061 GTACAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (15 bp):
AATAAATATAAGAAA
Found at i:19310 original size:29 final size:28
Alignment explanation
Indices: 19268--19369 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 28
19258 GTTCGGAGTA
* *
19268 AAAATATGTTTTTTGAGAAG-TCCGAGGC
1 AAAATGTGATTTTTG-GAAGATCCGAGGC
* *
19296 AAAAGTGTGATTTTTGGAAGATCGGGGGC
1 AAAA-TGTGATTTTTGGAAGATCCGAGGC
* * * *
19325 AAAATGTGA-TTTTGGAAGTTCGGGGGTA
1 AAAATGTGATTTTTGGAAGATCCGAGG-C
19353 AAAATGTGA-TTTTGGAA
1 AAAATGTGATTTTTGGAA
19370 AAATTTGGGG
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
27 16 0.25
28 30 0.46
29 19 0.29
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (28 bp):
AAAATGTGATTTTTGGAAGATCCGAGGC
Found at i:19347 original size:27 final size:27
Alignment explanation
Indices: 19293--19369 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 27
19283 AGAAGTCCGA
19293 GGCAAAAGTGTGATTTTTGGAAGATCGGG
1 GGCAAAA-TGTGA-TTTTGGAAGATCGGG
*
19322 GGCAAAATGTGATTTTGGAAGTTCGGG
1 GGCAAAATGTGATTTTGGAAGATCGGG
*
19349 GGTAAAAATGTGATTTTGGAA
1 GG-CAAAATGTGATTTTGGAA
19370 AAATTTGGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 16 0.36
28 22 0.49
29 7 0.16
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (27 bp):
GGCAAAATGTGATTTTGGAAGATCGGG
Found at i:25351 original size:17 final size:17
Alignment explanation
Indices: 25331--25371 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
25321 TGGGTTGAGA
* *
25331 AAATAATTTAATTGAAT
1 AAATAATTAAATTAAAT
*
25348 AAATAAATAAATTAAAT
1 AAATAATTAAATTAAAT
25365 AAATAAT
1 AAATAAT
25372 ATTTTGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATAATTAAATTAAAT
Found at i:34087 original size:8 final size:8
Alignment explanation
Indices: 34074--34099 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
34064 CGACGTACCT
34074 TTTCCAAA
1 TTTCCAAA
34082 TTTCCAAA
1 TTTCCAAA
34090 TTTCCAAA
1 TTTCCAAA
34098 TT
1 TT
34100 GGGTGGCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (8 bp):
TTTCCAAA
Found at i:40189 original size:22 final size:23
Alignment explanation
Indices: 40164--40221 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 23
40154 ATTTGCGCTA
*
40164 TGTGCGCCTACT-AATTGCACTG
1 TGTGCGCCTACTGAATTACACTG
* * *
40186 TGTGTGCTTACTGGATTACACTG
1 TGTGCGCCTACTGAATTACACTG
* *
40209 TGTGTGCTTACTG
1 TGTGCGCCTACTG
40222 TTTCCCCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.38
Consensus pattern (23 bp):
TGTGCGCCTACTGAATTACACTG
Found at i:41364 original size:26 final size:26
Alignment explanation
Indices: 41323--41374 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
41313 TCTGTTCCTC
41323 ATTTTTTATAAAAAAACCCTAGATTTG
1 ATTTTTTATAAAAAAACCCTAG-TTTG
* *
41350 ATTTTTTAT-ACAAAATCCTAGTTTG
1 ATTTTTTATAAAAAAACCCTAGTTTG
41375 GGGTTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
27 9 0.39
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTTTTTATAAAAAAACCCTAGTTTG
Found at i:41476 original size:33 final size:33
Alignment explanation
Indices: 41434--41498 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
41424 TTTCTTGTTG
41434 TTGTTTTTCTCCTCTTAAAACGATGAAACTAAA
1 TTGTTTTTCTCCTCTTAAAACGATGAAACTAAA
41467 TTGTTTTTCTCCTCTTAAAACGATGAAACTAA
1 TTGTTTTTCTCCTCTTAAAACGATGAAACTAA
41499 CTTCATCAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (33 bp):
TTGTTTTTCTCCTCTTAAAACGATGAAACTAAA
Found at i:44331 original size:20 final size:20
Alignment explanation
Indices: 44306--44346 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44296 ATGATAATTG
44306 TTCTCGAGTCCCCTTCCACT
1 TTCTCGAGTCCCCTTCCACT
44326 TTCTCGAGTCCCCTTCCACT
1 TTCTCGAGTCCCCTTCCACT
44346 T
1 T
44347 CTATATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.44, G:0.10, T:0.37
Consensus pattern (20 bp):
TTCTCGAGTCCCCTTCCACT
Found at i:55312 original size:22 final size:22
Alignment explanation
Indices: 55264--55305 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55254 ACAATAAAAA
* * *
55264 TAAAATAGTAGTAACATAATAG
1 TAAAATAGTAGAAAAACAATAG
55286 TAAAATAGTAGAAAAACAAT
1 TAAAATAGTAGAAAAACAAT
55306 GAGAAAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (22 bp):
TAAAATAGTAGAAAAACAATAG
Found at i:57910 original size:24 final size:26
Alignment explanation
Indices: 57883--57930 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
57873 AGAGAAATGT
57883 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
57907 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
57931 TCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:58023 original size:23 final size:23
Alignment explanation
Indices: 57993--58045 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
57983 ACGCTAGCGC
57993 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
** *
58016 GCTTACTGTTTTGCACTTTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
58039 GCTTACT
1 GCTTACT
58046 ATTTCGCACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGT
Found at i:58054 original size:23 final size:23
Alignment explanation
Indices: 58005--58063 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
57995 TTACTGTTCA
* * *
58005 GCACTGTGTGTGCTTACTGTTTT
1 GCACTTTGTGTGCTTACTATTTC
58028 GCACTTTGTGTGCTTACTATTTC
1 GCACTTTGTGTGCTTACTATTTC
* *
58051 GCACCTCGTGTGC
1 GCACTTTGTGTGC
58064 CTATTGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (23 bp):
GCACTTTGTGTGCTTACTATTTC
Found at i:58075 original size:46 final size:47
Alignment explanation
Indices: 58025--58142 Score: 104
Period size: 46 Copynumber: 2.6 Consensus size: 47
58015 TGCTTACTGT
*
58025 TTTGCACTTTGTGTGCTTACTATTTCGCACCT-CGTGTGCCTATT-GA
1 TTTGCACTATGTGTGCTTACTATTTCGCA-CTACGTGTGCCTATTGGA
* * *
58071 TTTGCGA-TATGTGAGCCTACTGGA-TT-GCACTATGTGTGCCTATTGGA
1 TTTGC-ACTATGTGTGCTTACT--ATTTCGCACTACGTGTGCCTATTGGA
* *
58118 -TTGCACTGTGTGTGCTTACTGTTTC
1 TTTGCACTATGTGTGCTTACTATTTC
58143 CCCAGCACTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
45 5 0.09
46 45 0.80
47 5 0.09
48 1 0.02
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (47 bp):
TTTGCACTATGTGTGCTTACTATTTCGCACTACGTGTGCCTATTGGA
Found at i:58130 original size:23 final size:23
Alignment explanation
Indices: 58058--58132 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
58048 TTCGCACCTC
58058 GTGTGCCTATT-GATTTGCGA-TAT
1 GTGTGCCTATTGGA-TTGC-ACTAT
* *
58081 GTGAGCCTACTGGATTGCACTAT
1 GTGTGCCTATTGGATTGCACTAT
*
58104 GTGTGCCTATTGGATTGCACTGT
1 GTGTGCCTATTGGATTGCACTAT
58127 GTGTGC
1 GTGTGC
58133 TTACTGTTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
22 1 0.02
23 42 0.93
24 2 0.04
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.37
Consensus pattern (23 bp):
GTGTGCCTATTGGATTGCACTAT
Found at i:61107 original size:15 final size:15
Alignment explanation
Indices: 61089--61135 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
61079 AATGGACAAA
61089 AAAAATAAACAAGAG
1 AAAAATAAACAAGAG
* *
61104 AAAAAAAAACAA-AA
1 AAAAATAAACAAGAG
61118 AAGAAATAAAGCAAGAG
1 AA-AAATAAA-CAAGAG
61135 A
1 A
61136 GCACTTTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 17 0.68
16 3 0.12
17 2 0.08
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.04
Consensus pattern (15 bp):
AAAAATAAACAAGAG
Found at i:61446 original size:29 final size:28
Alignment explanation
Indices: 61401--61461 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
61391 TTTACATTTG
*
61401 ATAAATATAATTGTTTATGTAT-TTAATA
1 ATAAATATAAATGTTTAT-TATATTAATA
61429 TATAAATATAAAAT-TTTATTATATTAATA
1 -ATAAATAT-AAATGTTTATTATATTAATA
61458 ATAA
1 ATAA
61462 TCATGATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 7 0.24
29 19 0.66
30 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (28 bp):
ATAAATATAAATGTTTATTATATTAATA
Found at i:61555 original size:33 final size:29
Alignment explanation
Indices: 61478--61542 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
61468 TGATTTGTGA
* *
61478 AAATCAAATCAAAATTTATATATAATATT
1 AAATAAAATCAAAATTTATATACAATATT
* *
61507 TATTAAAATCAAAATTTATATTACAATATT
1 AAATAAAATCAAAATTTATA-TACAATATT
61537 AAATAA
1 AAATAA
61543 TTGAATCAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATAAAATCAAAATTTATATACAATATT
Found at i:69976 original size:29 final size:29
Alignment explanation
Indices: 69927--69993 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
69917 ACAATTAATG
*
69927 AAAATA-ATAAAATGCGTATAATAAAATT
1 AAAATATATAAAATGCGCATAATAAAATT
* *
69955 AAAATATATAAGATGTGCATAATAAAATT
1 AAAATATATAAAATGCGCATAATAAAATT
*
69984 AAAATGTATA
1 AAAATATATA
69994 TATATGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (29 bp):
AAAATATATAAAATGCGCATAATAAAATT
Found at i:87405 original size:201 final size:191
Alignment explanation
Indices: 87074--87433 Score: 495
Period size: 201 Copynumber: 1.8 Consensus size: 191
87064 TATTCTCTAA
* * * * *
87074 CAATGCTGCTCACATGAGCTGTCGAGAGTATGTAATAAGCATAGTCCCAGCCATCGTAGGGCCTA
1 CAATGCTGCTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCCAGCCATCGTAAGGCCTA
* *
87139 TAATCCATTTAGGATCCATATCTCTTTCTCGAGTCACAATGCTGCTCACACGAGCTGTCGAGGAC
66 TAATCCATTTAGGATCCATATCTCTTTCCCGACTCACAATGCTGCTCACACGAGCTGTCGAGGAC
*
87204 TCGCAACATATACGATACCTCAGCCATCGATACGGTATTTGTGCATATAACTGTTCCTTAC
131 TCACAACATATACGATACCTCAGCCATCGATACGGTATTTGTGCATATAACTGTTCCTTAC
* * *
87265 CAATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAATCTCAGCCATCGTAAGGCC
1 CAATGCTGCTCACACGAGCTGTCGAGAATATGCA-ATAAGCAT-AATCCCAGCCATCGTAAGGCC
*
87330 TGTAATCCATTTAGGATCCATATTTCTTTTCTCAATTCCCGACTCACAATGCTGCTCACACGAGC
64 TATAATCCATTTAGGATCCATA--TC---TCT---TTCCCGACTCACAATGCTGCTCACACGAGC
* * *
87395 TGTTGAGGACTCACAACATATGCGGTACCTCAGCCATCG
121 TGTCGAGGACTCACAACATATACGATACCTCAGCCATCG
87434 CGTCGGTTTC
Statistics
Matches: 144, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
191 31 0.22
192 6 0.04
193 39 0.27
195 2 0.01
198 3 0.02
201 63 0.44
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (191 bp):
CAATGCTGCTCACACGAGCTGTCGAGAATATGCAATAAGCATAATCCCAGCCATCGTAAGGCCTA
TAATCCATTTAGGATCCATATCTCTTTCCCGACTCACAATGCTGCTCACACGAGCTGTCGAGGAC
TCACAACATATACGATACCTCAGCCATCGATACGGTATTTGTGCATATAACTGTTCCTTAC
Found at i:89907 original size:89 final size:89
Alignment explanation
Indices: 89756--89935 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 89
89746 AAGATGTTTT
89756 CTGTGGTGGCACGGCTGAAGCACAATCTACTTACAAATGTCGCAAACAGACCAACATATCAGACA
1 CTGTGGTGGCACGGCTGAAGCACAATCTACTTACAAATGTCGCAAACAGACCAACATATCAGACA
*
89821 GATCACTAGGACAGAAGAGTAGAA
66 GAACACTAGGACAGAAGAGTAGAA
89845 CTGTGGTGGCACGGCTGAAGCACAATCTACTTACAAATGTCGCAAACAGACCAACATATCAGACA
1 CTGTGGTGGCACGGCTGAAGCACAATCTACTTACAAATGTCGCAAACAGACCAACATATCAGACA
89910 GAACACTAGGACAGAAGAGTAGAA
66 GAACACTAGGACAGAAGAGTAGAA
89934 CT
1 CT
89936 CATAAGAGTG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (89 bp):
CTGTGGTGGCACGGCTGAAGCACAATCTACTTACAAATGTCGCAAACAGACCAACATATCAGACA
GAACACTAGGACAGAAGAGTAGAA
Found at i:92447 original size:16 final size:17
Alignment explanation
Indices: 92426--92472 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
92416 TTTTCCTCTA
92426 AAAAATATTAAATAA-T
1 AAAAATATTAAATAATT
* *
92442 AAAAATAGTAACTAATT
1 AAAAATATTAAATAATT
*
92459 AAATATAGTTAAAT
1 AAAAATA-TTAAAT
92473 TTTGATCCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 13 0.54
17 7 0.29
18 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
AAAAATATTAAATAATT
Found at i:94790 original size:24 final size:25
Alignment explanation
Indices: 94763--94813 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
94753 CTTCAGTTAT
94763 AGGAGCTATTTTAC-TTTATACTCA
1 AGGAGCTATTTTACTTTTATACTCA
* * *
94787 AGGATCTGTTTTACTTTTATATTCA
1 AGGAGCTATTTTACTTTTATACTCA
94812 AG
1 AG
94814 TGCTAGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (25 bp):
AGGAGCTATTTTACTTTTATACTCA
Found at i:99689 original size:57 final size:57
Alignment explanation
Indices: 99587--99695 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
99577 GCTTGTTAGT
* *
99587 GTTCAGATTCTGAGTAAATGCTTTTATCTGAATTAATATAATTTCTTTATAATTGTGC
1 GTTCAGATTCTGAGTAAATGCTTTTATCTGAACTAACATAATTTC-TTATAATTGTGC
* * *
99645 GTTCAGATTTTGA-TAAATGCTTTTATCT-AAGCTGACATAGTTTCTTATAAT
1 GTTCAGATTCTGAGTAAATGCTTTTATCTGAA-CTAACATAATTTCTTATAAT
99696 CTTGCAGATG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
56 9 0.20
57 24 0.53
58 12 0.27
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (57 bp):
GTTCAGATTCTGAGTAAATGCTTTTATCTGAACTAACATAATTTCTTATAATTGTGC
Found at i:103334 original size:34 final size:35
Alignment explanation
Indices: 103270--103352 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
103260 GATTTAAAGT
103270 AAAAAAAATGATAAAAACTATACATTAATAATATG
1 AAAAAAAATGATAAAAACTATACATTAATAATATG
* *
103305 AAAAAAAATTATTAAAA-TAT-CATTAAATAAT-T-
1 AAAAAAAATGATAAAAACTATACATT-AATAATATG
*
103337 AAAAATAAATCATAAA
1 AAAAA-AAATGATAAA
103353 TAATATAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
32 5 0.12
33 13 0.31
34 9 0.21
35 15 0.36
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (35 bp):
AAAAAAAATGATAAAAACTATACATTAATAATATG
Found at i:103358 original size:34 final size:33
Alignment explanation
Indices: 103269--103359 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 33
103259 AGATTTAAAG
*
103269 TAAAAAAAATGATAAAAACTATACATTAATAATA
1 TAAAAAAAATCATAAAAA-TATACATTAATAATA
* *
103303 TGAAAAAAAATTATTAAAATAT-CATTAAATAAT-
1 T-AAAAAAAATCATAAAAATATACATT-AATAATA
103336 TAAAAATAAATCATAAATAATATA
1 TAAAAA-AAATCATAAA-AATATA
103360 ATAGAAATGA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
32 5 0.10
33 13 0.27
34 15 0.31
35 15 0.31
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (33 bp):
TAAAAAAAATCATAAAAATATACATTAATAATA
Found at i:107873 original size:30 final size:30
Alignment explanation
Indices: 107839--107898 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
107829 CTAGGCCTTC
107839 ATTCATCATTGTATATAAAGTACCCCTTTT
1 ATTCATCATTGTATATAAAGTACCCCTTTT
107869 ATTCATCATTGTATATAAAGTACCCCTTTT
1 ATTCATCATTGTATATAAAGTACCCCTTTT
107899 TCAAGATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (30 bp):
ATTCATCATTGTATATAAAGTACCCCTTTT
Found at i:121423 original size:25 final size:25
Alignment explanation
Indices: 121389--121445 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
121379 ATGGTTACCA
* *
121389 TTTAACAATTAATAAATTTTTA-ATT
1 TTTAAAAATTAA-AAATTATTATATT
121414 TTTAAAAATTAAAAATTATTATATT
1 TTTAAAAATTAAAAATTATTATATT
*
121439 ATTAAAA
1 TTTAAAA
121446 GACGTATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTAAAAATTAAAAATTATTATATT
Found at i:122016 original size:16 final size:16
Alignment explanation
Indices: 121995--122036 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
121985 GTAAAAACTC
121995 AAAAAAAATT-ATATA
1 AAAAAAAATTAATATA
*
122010 AAAAAAAATTAAT-TT
1 AAAAAAAATTAATATA
122025 AAAAAAAATTAA
1 AAAAAAAATTAA
122037 AAAGATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 23 0.92
16 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAAAAATTAATATA
Found at i:122520 original size:17 final size:18
Alignment explanation
Indices: 122493--122527 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
122483 TATAACAATT
*
122493 ATTTTTATAACATTTAAA
1 ATTTTTATAACATATAAA
122511 ATTTTT-TAACATATAAA
1 ATTTTTATAACATATAAA
122528 TGAGACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTTATAACATATAAA
Found at i:123370 original size:17 final size:15
Alignment explanation
Indices: 123329--123361 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
123319 CTTGATTCTT
123329 AAAA-TTAAAAAAAA
1 AAAACTTAAAAAAAA
123343 AAAACTTAAAAAAATA
1 AAAACTTAAAAAAA-A
123359 AAA
1 AAA
123362 TATTTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 9 0.53
16 4 0.24
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAACTTAAAAAAAA
Found at i:124339 original size:31 final size:31
Alignment explanation
Indices: 124272--124339 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
124262 TGTAATATAT
* *
124272 TTAAATAATTTAACATAATAATATATGATAA
1 TTAAATAATTTAACATAATAATACATGAAAA
* *
124303 TTAAATAATTTAATATAATGATACAT-AAAA
1 TTAAATAATTTAACATAATAATACATGAAAA
124333 TATAAAT
1 T-TAAAT
124340 TAATCTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.12
31 28 0.88
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (31 bp):
TTAAATAATTTAACATAATAATACATGAAAA
Found at i:127017 original size:16 final size:16
Alignment explanation
Indices: 126996--127036 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
126986 AAGTGAAAAG
126996 AAAATTAGAA-AGATGA
1 AAAATTA-AAGAGATGA
127012 AAAATTAAAGAGATGA
1 AAAATTAAAGAGATGA
*
127028 AAAAATAAA
1 AAAATTAAA
127037 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (16 bp):
AAAATTAAAGAGATGA
Found at i:130009 original size:7 final size:7
Alignment explanation
Indices: 129997--130025 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
129987 TGTCCCCTAT
129997 GTCTACA
1 GTCTACA
130004 GTCTACA
1 GTCTACA
130011 GTCTACA
1 GTCTACA
130018 GTCTACA
1 GTCTACA
130025 G
1 G
130026 AAGAGCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (7 bp):
GTCTACA
Found at i:131786 original size:21 final size:21
Alignment explanation
Indices: 131762--131803 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
131752 GACAGCAGCG
*
131762 TGACAAGGGGAGACGAGATGA
1 TGACAAGAGGAGACGAGATGA
*
131783 TGACGAGAGGAGACGAGATGA
1 TGACAAGAGGAGACGAGATGA
131804 GAATAGGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.43, T:0.10
Consensus pattern (21 bp):
TGACAAGAGGAGACGAGATGA
Found at i:140274 original size:15 final size:15
Alignment explanation
Indices: 140249--140281 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
140239 GCAAAAAGGC
140249 TTTTGAATTTTG-AA
1 TTTTGAATTTTGCAA
140263 TTTTGCAATTTTGCAA
1 TTTTG-AATTTTGCAA
140279 TTT
1 TTT
140282 GGTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTTGAATTTTGCAA
Found at i:140282 original size:7 final size:8
Alignment explanation
Indices: 140249--140281 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
140239 GCAAAAAGGC
140249 TTTTG-AA
1 TTTTGCAA
140256 TTTTG-AA
1 TTTTGCAA
140263 TTTTGCAA
1 TTTTGCAA
140271 TTTTGCAA
1 TTTTGCAA
140279 TTT
1 TTT
140282 GGTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 12 0.48
8 13 0.52
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.58
Consensus pattern (8 bp):
TTTTGCAA
Found at i:146480 original size:3 final size:3
Alignment explanation
Indices: 146474--146501 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
146464 TTTTATGGCT
146474 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
146502 TATGCTGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:153216 original size:14 final size:15
Alignment explanation
Indices: 153197--153235 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
153187 AAAACTCAAT
*
153197 TTTTTAAATA-TATA
1 TTTTTAAAAATTATA
153211 TTTTTAAAAATTATA
1 TTTTTAAAAATTATA
*
153226 ATTTTAAAAA
1 TTTTTAAAAA
153236 ATTAATATGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTTAAAAATTATA
Found at i:153236 original size:16 final size:17
Alignment explanation
Indices: 153205--153243 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
153195 ATTTTTTAAA
*
153205 TATATATTTTTAAAAAT
1 TATATATTTTAAAAAAT
153222 TATA-ATTTTAAAAAAT
1 TATATATTTTAAAAAAT
153238 TA-ATAT
1 TATATAT
153244 GGAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 15 0.75
17 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATATTTTAAAAAAT
Found at i:154342 original size:25 final size:25
Alignment explanation
Indices: 154297--154347 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
154287 TAAACTGAAA
* * *
154297 TTGATTGAATTAAATTATAAATAAT
1 TTGATTGAAATAAACTATAAACAAT
154322 TTGATTGAAAATAAACT-TAAACAAT
1 TTGATTG-AAATAAACTATAAACAAT
154347 T
1 T
154348 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (25 bp):
TTGATTGAAATAAACTATAAACAAT
Found at i:164211 original size:20 final size:20
Alignment explanation
Indices: 164174--164211 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
164164 TTTTGATTAA
*
164174 TTTAATTTTTTATGTTTTTT
1 TTTAATTTTTTATATTTTTT
164194 TTTAACTTTTTT-TATTTT
1 TTTAA-TTTTTTATATTTT
164212 ACATTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTAATTTTTTATATTTTTT
Found at i:171642 original size:2 final size:2
Alignment explanation
Indices: 171635--171675 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
171625 ATATTATCTA
171635 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
171676 GCATGAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:173375 original size:21 final size:21
Alignment explanation
Indices: 173303--173379 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
173293 GAATTCGAGA
*
173303 TTTAGGTTT-TGAATTTTATAT
1 TTTAGGTTTATG-ATTTTAGAT
* * *
173324 TTTAGGTTTAGGGTTTAAGAT
1 TTTAGGTTTATGATTTTAGAT
* *
173345 TCTAGATTTATGATTTTAGAT
1 TTTAGGTTTATGATTTTAGAT
*
173366 TTTGGGTTTA-GATT
1 TTTAGGTTTATGATT
173380 AAAAAAATAA
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
20 4 0.09
21 38 0.88
22 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.21, T:0.55
Consensus pattern (21 bp):
TTTAGGTTTATGATTTTAGAT
Found at i:174350 original size:44 final size:44
Alignment explanation
Indices: 174290--174379 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
174280 CTCTTTGGCA
*
174290 TCTGCTTTCAGCACTAGTGGTCGAGTACTTGATTCTTTTCGGAG
1 TCTGCTTTCAGCACTAGTGGTCGAGTACTTGATTCTTATCGGAG
* * *
174334 TCTGCTTTTAGTACTAGTGGTCGAGTACTTGATTCTTATCGTAG
1 TCTGCTTTCAGCACTAGTGGTCGAGTACTTGATTCTTATCGGAG
174378 TC
1 TC
174380 GACTTCTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (44 bp):
TCTGCTTTCAGCACTAGTGGTCGAGTACTTGATTCTTATCGGAG
Found at i:175562 original size:19 final size:18
Alignment explanation
Indices: 175540--175620 Score: 67
Period size: 17 Copynumber: 4.3 Consensus size: 18
175530 TTTATAAACT
175540 TATAAAAATTCTTAAAAAATA
1 TATAAAAATT-TT-AAAAA-A
175561 TATAAAAATTTTAAAAAA
1 TATAAAAATTTTAAAAAA
* * *
175579 AAT-AATATTCTAAAAAA
1 TATAAAAATTTTAAAAAA
*
175596 TAT-ATAATTTTAATAAAA
1 TATAAAAATTTTAA-AAAA
175614 TTATAAA
1 -TATAAA
175621 TATTAGAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
17 21 0.43
18 7 0.14
19 8 0.16
20 3 0.06
21 10 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAAAATTTTAAAAAA
Found at i:175565 original size:21 final size:21
Alignment explanation
Indices: 175540--175602 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 21
175530 TTTATAAACT
175540 TATAAAAATTCTTAAAAAATA
1 TATAAAAATTCTTAAAAAATA
175561 TATAAAAATT-TTAAAAAA-A
1 TATAAAAATTCTTAAAAAATA
*
175580 -AT-AATATTC-TAAAAAATA
1 TATAAAAATTCTTAAAAAATA
175598 TATAA
1 TATAA
175603 TTTTAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 12 0.32
18 3 0.08
19 3 0.08
20 9 0.24
21 10 0.27
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAAAATTCTTAAAAAATA
Found at i:177316 original size:2 final size:2
Alignment explanation
Indices: 177309--177342 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
177299 ATATTTTAAA
177309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177343 TAATTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:181478 original size:30 final size:30
Alignment explanation
Indices: 181437--181512 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
181427 CACCTGTTAG
* * * *
181437 TTCACCGCCACCATCATCGCAACCTCCCCT
1 TTCAACGCCACCACCAGCACAACCTCCCCT
181467 TTCAACGCCACCACCAGCACAACCTCCCCT
1 TTCAACGCCACCACCAGCACAACCTCCCCT
181497 TTCAACGCCACCACCA
1 TTCAACGCCACCACCA
181513 TTACGATCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.25, C:0.53, G:0.07, T:0.16
Consensus pattern (30 bp):
TTCAACGCCACCACCAGCACAACCTCCCCT
Found at i:200384 original size:8 final size:8
Alignment explanation
Indices: 200371--200414 Score: 88
Period size: 8 Copynumber: 5.5 Consensus size: 8
200361 CGTGGGTTGT
200371 GAAATAAA
1 GAAATAAA
200379 GAAATAAA
1 GAAATAAA
200387 GAAATAAA
1 GAAATAAA
200395 GAAATAAA
1 GAAATAAA
200403 GAAATAAA
1 GAAATAAA
200411 GAAA
1 GAAA
200415 ATGGAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
GAAATAAA
Found at i:200768 original size:19 final size:20
Alignment explanation
Indices: 200744--200782 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
200734 TGTACTCCAA
*
200744 TTTTCTTATGTTT-ATATAT
1 TTTTCTAATGTTTAATATAT
*
200763 TTTTCTAATTTTTAATATAT
1 TTTTCTAATGTTTAATATAT
200783 AATAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTCTAATGTTTAATATAT
Found at i:202209 original size:20 final size:21
Alignment explanation
Indices: 202172--202210 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
202162 ATTTTTTTAA
*
202172 TTTAAAAAATAATTTTAAAAT
1 TTTAAAAAATAATATTAAAAT
202193 TTTAAAAAATAA-ATTAAA
1 TTTAAAAAATAATATTAAA
202211 TGTTGACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTAAAAAATAATATTAAAAT
Found at i:203438 original size:11 final size:11
Alignment explanation
Indices: 203422--203459 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
203412 TCTAACTTTG
203422 AAAAATCATAA
1 AAAAATCATAA
*
203433 AAAAAT-ATAG
1 AAAAATCATAA
203443 AAAAATCATAA
1 AAAAATCATAA
203454 AAAAAT
1 AAAAAT
203460 ATAGAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.74, C:0.05, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAATCATAA
Found at i:203446 original size:10 final size:11
Alignment explanation
Indices: 203421--203465 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
203411 TTCTAACTTT
203421 GAAAAATCATA
1 GAAAAATCATA
*
203432 AAAAAAT-ATA
1 GAAAAATCATA
203442 GAAAAATCATA
1 GAAAAATCATA
*
203453 AAAAAAT-ATA
1 GAAAAATCATA
203463 GAA
1 GAA
203466 GGAGAAGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 14 0.48
11 15 0.52
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (11 bp):
GAAAAATCATA
Found at i:203447 original size:21 final size:21
Alignment explanation
Indices: 203421--203465 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
203411 TTCTAACTTT
203421 GAAAAATCATAAAAAAATATA
1 GAAAAATCATAAAAAAATATA
203442 GAAAAATCATAAAAAAATATA
1 GAAAAATCATAAAAAAATATA
203463 GAA
1 GAA
203466 GGAGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (21 bp):
GAAAAATCATAAAAAAATATA
Done.